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- PDB-7b58: X-ray crystal structure of Sporosarcina pasteurii urease inhibite... -

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Basic information

Entry
Database: PDB / ID: 7b58
TitleX-ray crystal structure of Sporosarcina pasteurii urease inhibited by Ag(PEt3)Cl determined at 1.72 Angstroms
Components(Urease subunit ...) x 3
KeywordsHYDROLASE / urease / enzyme / nickel / silver
Function / homology
Function and homology information


urease complex / urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm
Similarity search - Function
Urease, gamma subunit / Urease active site / Urease active site. / Urease nickel binding site / Urease nickel ligands signature. / Urease, beta subunit / Urease, alpha subunit / Urease alpha subunit, C-terminal / Urease, beta subunit superfamily / Urease beta subunit ...Urease, gamma subunit / Urease active site / Urease active site. / Urease nickel binding site / Urease nickel ligands signature. / Urease, beta subunit / Urease, alpha subunit / Urease alpha subunit, C-terminal / Urease, beta subunit superfamily / Urease beta subunit / Urease domain profile. / Urease alpha-subunit, N-terminal domain / Urease alpha-subunit, N-terminal domain / Urease, gamma/gamma-beta subunit / Urease, gamma subunit superfamily / Urease, gamma subunit / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolase
Similarity search - Domain/homology
SILVER ION / NICKEL (II) ION / OXYGEN ATOM / Urease subunit alpha / Urease subunit beta / Urease subunit gamma
Similarity search - Component
Biological speciesSporosarcina pasteurii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsMazzei, L. / Cianci, M. / Ciurli, S.
CitationJournal: J.Inorg.Biochem. / Year: 2021
Title: Kinetic and structural analysis of the inactivation of urease by mixed-ligand phosphine halide Ag(I) complexes.
Authors: Mazzei, L. / Cirri, D. / Cianci, M. / Messori, L. / Ciurli, S.
History
DepositionDec 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 2.0Apr 20, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Source and taxonomy
Category: atom_site / entity_src_nat ...atom_site / entity_src_nat / pdbx_nonpoly_scheme / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _entity_src_nat.common_name / _pdbx_nonpoly_scheme.auth_seq_num / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 2.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Urease subunit gamma
BBB: Urease subunit beta
CCC: Urease subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,15340
Polymers86,2403
Non-polymers2,91337
Water11,187621
1
AAA: Urease subunit gamma
BBB: Urease subunit beta
CCC: Urease subunit alpha
hetero molecules

AAA: Urease subunit gamma
BBB: Urease subunit beta
CCC: Urease subunit alpha
hetero molecules

AAA: Urease subunit gamma
BBB: Urease subunit beta
CCC: Urease subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)267,458120
Polymers258,7199
Non-polymers8,740111
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area68030 Å2
ΔGint-815 kcal/mol
Surface area59560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.441, 131.441, 189.759
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11AAA-207-

SO4

21AAA-207-

SO4

31CCC-616-

SO4

41CCC-624-

SO4

51CCC-624-

SO4

61CCC-765-

HOH

71CCC-989-

HOH

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Components

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Urease subunit ... , 3 types, 3 molecules AAABBBCCC

#1: Protein Urease subunit gamma / Urea amidohydrolase subunit gamma


Mass: 11134.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sporosarcina pasteurii (bacteria) / References: UniProt: P41022, urease
#2: Protein Urease subunit beta / Urea amidohydrolase subunit beta


Mass: 13529.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sporosarcina pasteurii (bacteria) / References: UniProt: P41021, urease
#3: Protein Urease subunit alpha / Urea amidohydrolase subunit alpha


Mass: 61575.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sporosarcina pasteurii (bacteria) / References: UniProt: P41020, urease

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Non-polymers , 6 types, 658 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#7: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O
#8: Chemical ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ag / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 621 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.51 % / Description: Rice-shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: THE PROTEIN-LIGAND (300 microM) COMPLEX IN 50 mM HEPES BUFFER, PH 7.50 (ALSO CONTAINING 1% (V/V) DMSO), DILUTED 1:1 WITH A SOLUTION OF 1.4 M AMMONIUM SULFATE ALSO CONTAINING THE SAME ...Details: THE PROTEIN-LIGAND (300 microM) COMPLEX IN 50 mM HEPES BUFFER, PH 7.50 (ALSO CONTAINING 1% (V/V) DMSO), DILUTED 1:1 WITH A SOLUTION OF 1.4 M AMMONIUM SULFATE ALSO CONTAINING THE SAME CONCENTRATION OF LIGAND AND DMSO.
PH range: 6.3-6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2019
RadiationMonochromator: SI(111) SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.72→189.76 Å / Num. obs: 102636 / % possible obs: 100 % / Redundancy: 19.6 % / Biso Wilson estimate: 27.5 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.044 / Rrim(I) all: 0.141 / Net I/σ(I): 19.3
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 20.3 % / Rmerge(I) obs: 4.03 / Mean I/σ(I) obs: 1 / Num. unique obs: 5029 / CC1/2: 0.699 / Rpim(I) all: 1.297 / Rrim(I) all: 4.235 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
REFMAC5.8.0258phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G48

6g48


Resolution: 1.72→72.989 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.973 / SU B: 2.915 / SU ML: 0.082 / Cross valid method: FREE R-VALUE / ESU R: 0.086 / ESU R Free: 0.087
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1852 5112 4.987 %random
Rwork0.1555 97390 --
all0.157 ---
obs-102502 99.904 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.389 Å2
Baniso -1Baniso -2Baniso -3
1-1.082 Å20.541 Å20 Å2
2--1.082 Å20 Å2
3----3.511 Å2
Refinement stepCycle: LAST / Resolution: 1.72→72.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6047 0 150 621 6818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0136471
X-RAY DIFFRACTIONr_bond_other_d0.0020.0176059
X-RAY DIFFRACTIONr_angle_refined_deg1.7081.6498768
X-RAY DIFFRACTIONr_angle_other_deg1.4241.59614103
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3595837
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.30123.012322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.371151121
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.411539
X-RAY DIFFRACTIONr_chiral_restr0.0850.2855
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027284
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021241
X-RAY DIFFRACTIONr_nbd_refined0.2060.21320
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.25896
X-RAY DIFFRACTIONr_nbtor_refined0.160.23021
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.22788
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2553
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.080.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2360.246
X-RAY DIFFRACTIONr_nbd_other0.1830.2256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1860.265
X-RAY DIFFRACTIONr_mcbond_it2.1843.0973259
X-RAY DIFFRACTIONr_mcbond_other2.1823.0973258
X-RAY DIFFRACTIONr_mcangle_it2.6494.6344098
X-RAY DIFFRACTIONr_mcangle_other2.6494.6344099
X-RAY DIFFRACTIONr_scbond_it3.8273.5383212
X-RAY DIFFRACTIONr_scbond_other3.3233.4163145
X-RAY DIFFRACTIONr_scangle_it5.4295.1844660
X-RAY DIFFRACTIONr_scangle_other4.6224.9914559
X-RAY DIFFRACTIONr_lrange_it7.8239.4217220
X-RAY DIFFRACTIONr_lrange_other7.45438.9297084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.7650.3543640.3317112X-RAY DIFFRACTION99.9465
1.765-1.8130.3063710.2996903X-RAY DIFFRACTION99.9725
1.813-1.8660.2873370.2696741X-RAY DIFFRACTION99.9294
1.866-1.9230.2513190.2366576X-RAY DIFFRACTION99.8986
1.923-1.9860.2513460.2296345X-RAY DIFFRACTION99.9552
1.986-2.0560.253010.2056188X-RAY DIFFRACTION99.9692
2.056-2.1330.2333020.1835941X-RAY DIFFRACTION99.968
2.133-2.220.1863030.1645730X-RAY DIFFRACTION99.8841
2.22-2.3190.2113150.1595484X-RAY DIFFRACTION99.8966
2.319-2.4320.2012740.1485274X-RAY DIFFRACTION99.874
2.432-2.5640.1872530.1425022X-RAY DIFFRACTION99.9432
2.564-2.7190.1672520.1384760X-RAY DIFFRACTION99.8406
2.719-2.9070.192250.1364492X-RAY DIFFRACTION99.9364
2.907-3.1390.1862570.1434172X-RAY DIFFRACTION99.7747
3.139-3.4390.1812030.153869X-RAY DIFFRACTION99.8529
3.439-3.8440.1491810.1323546X-RAY DIFFRACTION99.9196
3.844-4.4380.1351560.1093149X-RAY DIFFRACTION99.7284
4.438-5.4340.1351520.1072689X-RAY DIFFRACTION99.9297
5.434-7.6750.1421220.1272128X-RAY DIFFRACTION100
7.675-100.164790.1621269X-RAY DIFFRACTION99.2636

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